Vertebrates have evolved within a world dominated by microorganisms, and the vertebrate microflora consequently plays important roles in gut development and physiology. However, the mechanisms that underlie these host-microbial interactions remain almost entirely unknown. The zebrafish provides new opportunities to investigate these processes using forward genetic analysis, and in vivo observation of the developing gut and its inhabitants. The goal of this proposal is to reveal the impact of microbes on zebrafish gut biology. First, zebrafish will be reared free of any microbes (germ-free or gnotobiotic zebrafish), and the morphology of germ-free and conventionally-raised zebrafish intestines will be compared. Second, the range of host processes affected by the microflora will be revealed through a functional genomic comparison of gene expression in the intestines of germ-free and conventionally-raised zebrafish. Third, host responsiveness to microbial colonization will be assayed by similarly analyzing the response of germ-free zebrafish to selected microbial species. This proposed research would provide a foundation for future analysis of the host and microbial mechanisms that regulate the rich ecosystem within the vertebrate digestive tract.